Affiliation: Division of Parasitology, New England Biolabs, Inc, Ipswich, Massachusetts, United States of America. foster@neb.com

ABSTRACT

Background: The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE) having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms.

Methods/principal findings: To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM mutants in E. coli and discovered the ΔdPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect.

Conclusions/significance: Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.

pone-0013576-g002: Distribution of PGM types across 96 completed genome sequences from the Class Bacilli.Taxonomic nodes (left to right) are Class, Order, Family, Genus. Taxa with genomes containing only iPGM are shaded yellow, those with only dPGM are shaded blue, those with both iPGM and dPGM are shaded green while taxa with non-uniform PGM profiles are shaded pink. The numbers in boxes accompanying each taxon identifier correspond to (left to right) number of genomes with only dPGM, only iPGM, both dPGM and iPGM, and no PGM.

Mentions:
We found that much of the PGM heterogeneity observed in certain classes of bacteria (Table 1) stratified when individual families and genera were considered. For example, the diversity observed in the class Bacilli (Table 1) was resolved by examination of different families and genera (Fig. 2). Although a comparison between different families or genera revealed divergent PGM profiles, of 9 represented families, only the Bacillaceae exhibited diversity within its PGM profile, and of 13 genera, only the genus Bacillus (6 iPGM; 10 iPGM plus dPGM) had a non-uniform distribution (Fig. 2). Similarly, the 66 genomes from the family Enterobacteriaceae (γ-proteobacteria) (12 dPGM; 54 dPGM + iPGM) come from 17 genera, each of which is internally homogeneous: either a genus had exclusively dPGM or it had dPGM plus iPGM (Fig. S1). Nonetheless, the different lineages within the classes Bacilli and γ-proteobacteria still showed considerable variation in their PGM profiles, as depicted by the shading in Fig. 2 and Fig. S1. For example, of the 3 species within the family Alteromonadaceae (γ-proteobacteria), one contains dPGM, another contains iPGM and the third contains both. Variation also existed even at the species level: of two species of Pseudoalteromonas (γ-proteobacteria), one contains iPGM while the other has both dPGM and iPGM (Fig. S1, Table S1). Other classes of bacteria such as the Clostridia and α-proteobacteria showed yet more variation in their PGM profiles (Figs 3, 4). All 19 Clostridium spp. genomes contain iPGM but 3 of these additionally contain dPGM. Similarly, amongst the 7 genomes within the order Thermoanaerobacterales (Clostridia) examples exist of those containing just dPGM or iPGM or both. All 3 species of Thermoanaerobacter contain dPGM but 2 of them also have iPGM (Fig. 3, Table S1). The order Rhizobiales (α-proteobacteria) has a particularly haphazard PGM distribution with individual species in 2 genera (Bradyrhizobium and Methylobacterium) showing variable PGM profiles. However, the iPGM identified in Bradyrhizobium sp. BTAi1 consists of only the N-terminal 225 amino acids and is followed by a transposase so we considered it a pseudogene. Of the 6 sequenced strains of Rhodopseudomonas palustris, 4 contain only iPGM while the remaining 2 have only dPGM (Fig. 4, Table S1). Strains of this species are known to have variable gene contents and the two strains that contain only dPGM are more similar to each other than to the other isolates [30]. Other classes of bacteria showed variable levels of PGM heterogeneity (Tables 1, S1). Of 53 Actinobacteria genomes all but 2 contain solely dPGM. However, Rubrobacter xylanophilus contains iPGM of archaeal origin as its only PGM, while Streptomyces coelicolor has both bacterial iPGM and dPGM. The sister species, S. avermitilis and S. griseus, have only dPGM. Within the δ-proteobacteria, a similar species-level variability was observed in the genus Geobacter where all 5 sequenced genomes encode both bacterial and archaeal iPGM, but 3 genomes additionally contain dPGM. A further interesting example of PGM diversity was seen between the two Candidatus Phytoplasma spp. (Mollicutes). Candidatus P. australiense has iPGM and an intact glycolytic pathway, whereas Candidatus P. mali has an incomplete glycolytic pathway that terminates in glyceraldehyde-3-phosphate and consequently lacks any form of PGM.

pone-0013576-g002: Distribution of PGM types across 96 completed genome sequences from the Class Bacilli.Taxonomic nodes (left to right) are Class, Order, Family, Genus. Taxa with genomes containing only iPGM are shaded yellow, those with only dPGM are shaded blue, those with both iPGM and dPGM are shaded green while taxa with non-uniform PGM profiles are shaded pink. The numbers in boxes accompanying each taxon identifier correspond to (left to right) number of genomes with only dPGM, only iPGM, both dPGM and iPGM, and no PGM.

Mentions:
We found that much of the PGM heterogeneity observed in certain classes of bacteria (Table 1) stratified when individual families and genera were considered. For example, the diversity observed in the class Bacilli (Table 1) was resolved by examination of different families and genera (Fig. 2). Although a comparison between different families or genera revealed divergent PGM profiles, of 9 represented families, only the Bacillaceae exhibited diversity within its PGM profile, and of 13 genera, only the genus Bacillus (6 iPGM; 10 iPGM plus dPGM) had a non-uniform distribution (Fig. 2). Similarly, the 66 genomes from the family Enterobacteriaceae (γ-proteobacteria) (12 dPGM; 54 dPGM + iPGM) come from 17 genera, each of which is internally homogeneous: either a genus had exclusively dPGM or it had dPGM plus iPGM (Fig. S1). Nonetheless, the different lineages within the classes Bacilli and γ-proteobacteria still showed considerable variation in their PGM profiles, as depicted by the shading in Fig. 2 and Fig. S1. For example, of the 3 species within the family Alteromonadaceae (γ-proteobacteria), one contains dPGM, another contains iPGM and the third contains both. Variation also existed even at the species level: of two species of Pseudoalteromonas (γ-proteobacteria), one contains iPGM while the other has both dPGM and iPGM (Fig. S1, Table S1). Other classes of bacteria such as the Clostridia and α-proteobacteria showed yet more variation in their PGM profiles (Figs 3, 4). All 19 Clostridium spp. genomes contain iPGM but 3 of these additionally contain dPGM. Similarly, amongst the 7 genomes within the order Thermoanaerobacterales (Clostridia) examples exist of those containing just dPGM or iPGM or both. All 3 species of Thermoanaerobacter contain dPGM but 2 of them also have iPGM (Fig. 3, Table S1). The order Rhizobiales (α-proteobacteria) has a particularly haphazard PGM distribution with individual species in 2 genera (Bradyrhizobium and Methylobacterium) showing variable PGM profiles. However, the iPGM identified in Bradyrhizobium sp. BTAi1 consists of only the N-terminal 225 amino acids and is followed by a transposase so we considered it a pseudogene. Of the 6 sequenced strains of Rhodopseudomonas palustris, 4 contain only iPGM while the remaining 2 have only dPGM (Fig. 4, Table S1). Strains of this species are known to have variable gene contents and the two strains that contain only dPGM are more similar to each other than to the other isolates [30]. Other classes of bacteria showed variable levels of PGM heterogeneity (Tables 1, S1). Of 53 Actinobacteria genomes all but 2 contain solely dPGM. However, Rubrobacter xylanophilus contains iPGM of archaeal origin as its only PGM, while Streptomyces coelicolor has both bacterial iPGM and dPGM. The sister species, S. avermitilis and S. griseus, have only dPGM. Within the δ-proteobacteria, a similar species-level variability was observed in the genus Geobacter where all 5 sequenced genomes encode both bacterial and archaeal iPGM, but 3 genomes additionally contain dPGM. A further interesting example of PGM diversity was seen between the two Candidatus Phytoplasma spp. (Mollicutes). Candidatus P. australiense has iPGM and an intact glycolytic pathway, whereas Candidatus P. mali has an incomplete glycolytic pathway that terminates in glyceraldehyde-3-phosphate and consequently lacks any form of PGM.

Bottom Line:
Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not.Metabolic redundancy is indicated since only larger genomes encode both forms.Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.

Affiliation:
Division of Parasitology, New England Biolabs, Inc, Ipswich, Massachusetts, United States of America. foster@neb.com

ABSTRACT

Background: The glycolytic phosphoglycerate mutases exist as non-homologous isofunctional enzymes (NISE) having independent evolutionary origins and no similarity in primary sequence, 3D structure, or catalytic mechanism. Cofactor-dependent PGM (dPGM) requires 2,3-bisphosphoglycerate for activity; cofactor-independent PGM (iPGM) does not. The PGM profile of any given bacterium is unpredictable and some organisms such as Escherichia coli encode both forms.

Methods/principal findings: To examine the distribution of PGM NISE throughout the Bacteria, and gain insight into the evolutionary processes that shape their phyletic profiles, we searched bacterial genome sequences for the presence of dPGM and iPGM. Both forms exhibited patchy distributions throughout the bacterial domain. Species within the same genus, or even strains of the same species, frequently differ in their PGM repertoire. The distribution is further complicated by the common occurrence of dPGM paralogs, while iPGM paralogs are rare. Larger genomes are more likely to accommodate PGM paralogs or both NISE forms. Lateral gene transfers have shaped the PGM profiles with intradomain and interdomain transfers apparent. Archaeal-type iPGM was identified in many bacteria, often as the sole PGM. To address the function of PGM NISE in an organism encoding both forms, we analyzed recombinant enzymes from E. coli. Both NISE were active mutases, but the specific activity of dPGM greatly exceeded that of iPGM, which showed highest activity in the presence of manganese. We created PGM mutants in E. coli and discovered the ΔdPGM mutant grew slowly due to a delay in exiting stationary phase. Overexpression of dPGM or iPGM overcame this defect.

Conclusions/significance: Our biochemical and genetic analyses in E. coli firmly establish dPGM and iPGM as NISE. Metabolic redundancy is indicated since only larger genomes encode both forms. Non-orthologous gene displacement can fully account for the non-uniform PGM distribution we report across the bacterial domain.